Scunthorpe fans are being asked to fork out £18 for a full-price ticket, while the Premiership club are only asking for £15 from supporters who purchase a ticket in advance.
It follows an intervention by the Football Association, who set the price at £18 after the two clubs failed to agree a fee - with the home side thought to favour a lower price to encourage a bigger gate.
United confirmed their position on Thursday after criticism of the price difference on the Iron-Bru.net messageboard.
The wrangling caused days of delay in announcing the ticket allocation, even though the number of tickets was quickly agreed.
City believed in the lower price, hence them offering a reduced price to their own support - although they will still have to contribute an extra £3 per person to the pot to the FA's prize fund.